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Merged
stain merged 2 commits into from
Aug 23, 2017
Merged

Fix for invalid branch names being accepted in some circumstances #165

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ada4941
Fix for invalid branch names being accepted in some circumstances
MarkRobbo Aug 23, 2017
fcf9044
Fix regression in supporting slashes in branch names
MarkRobbo Aug 23, 2017
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96 changes: 42 additions & 54 deletions src/main/java/org/commonwl/view/git/GitService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,6 @@
import org.commonwl.view.researchobject.HashableAgent;
import org.eclipse.jgit.api.Git;
import org.eclipse.jgit.api.errors.GitAPIException;
import org.eclipse.jgit.api.errors.RefNotFoundException;
import org.eclipse.jgit.lib.ObjectId;
import org.eclipse.jgit.lib.PersonIdent;
import org.eclipse.jgit.revwalk.RevCommit;
Expand Down Expand Up @@ -72,59 +71,47 @@ public GitService(@Value("${gitStorage}") Path gitStorage,
*/
public Git getRepository(GitDetails gitDetails, boolean reuseDir)
throws GitAPIException, IOException {
Git repo = null;
while (repo == null) {
try {
if (reuseDir) {
// Base dir from configuration, name from hash of repository URL
String baseName = DigestUtils.sha1Hex(GitDetails.normaliseUrl(gitDetails.getRepoUrl()));

// Check if folder already exists
Path repoDir = gitStorage.resolve(baseName);
if (Files.isReadable(repoDir) && Files.isDirectory(repoDir)) {
repo = Git.open(repoDir.toFile());
repo.fetch().call();
} else {
// Create a folder and clone repository into it
Files.createDirectory(repoDir);
repo = Git.cloneRepository()
.setCloneSubmodules(cloneSubmodules)
.setURI(gitDetails.getRepoUrl())
.setDirectory(repoDir.toFile())
.setCloneAllBranches(true)
.call();
}
} else {
// Another thread is already using the existing folder
// Must create another temporary one
repo = Git.cloneRepository()
.setCloneSubmodules(cloneSubmodules)
.setURI(gitDetails.getRepoUrl())
.setDirectory(createTempDir())
.setCloneAllBranches(true)
.call();
}
Git repo;
if (reuseDir) {
// Base dir from configuration, name from hash of repository URL
String baseName = DigestUtils.sha1Hex(GitDetails.normaliseUrl(gitDetails.getRepoUrl()));

// Check if folder already exists
Path repoDir = gitStorage.resolve(baseName);
if (Files.isReadable(repoDir) && Files.isDirectory(repoDir)) {
repo = Git.open(repoDir.toFile());
repo.fetch().call();
} else {
// Create a folder and clone repository into it
Files.createDirectory(repoDir);
repo = Git.cloneRepository()
.setCloneSubmodules(cloneSubmodules)
.setURI(gitDetails.getRepoUrl())
.setDirectory(repoDir.toFile())
.setCloneAllBranches(true)
.call();
}
} else {
// Another thread is already using the existing folder
// Must create another temporary one
repo = Git.cloneRepository()
.setCloneSubmodules(cloneSubmodules)
.setURI(gitDetails.getRepoUrl())
.setDirectory(createTempDir())
.setCloneAllBranches(true)
.call();
}

// Checkout the specific branch or commit ID
if (repo != null) {
// Create a new local branch if it does not exist and not a commit ID
String branchOrCommitId = gitDetails.getBranch();
if (!ObjectId.isId(branchOrCommitId)) {
branchOrCommitId = "refs/remotes/origin/" + branchOrCommitId;
}
repo.checkout()
.setName(branchOrCommitId)
.call();
}
} catch (RefNotFoundException ex) {
// Attempt slashes in branch fix
GitDetails correctedForSlash = transferPathToBranch(gitDetails);
if (correctedForSlash != null) {
gitDetails = correctedForSlash;
} else {
throw ex;
}
// Checkout the specific branch or commit ID
if (repo != null) {
// Create a new local branch if it does not exist and not a commit ID
String branchOrCommitId = gitDetails.getBranch();
if (!ObjectId.isId(branchOrCommitId)) {
branchOrCommitId = "refs/remotes/origin/" + branchOrCommitId;
}
repo.checkout()
.setName(branchOrCommitId)
.call();
}

return repo;
Expand Down Expand Up @@ -189,8 +176,9 @@ public GitDetails transferPathToBranch(GitDetails githubInfo) {
if (firstSlash > 0) {
branch += "/" + path.substring(0, firstSlash);
path = path.substring(firstSlash + 1);
return new GitDetails(githubInfo.getRepoUrl(), branch,
path);
GitDetails newDetails = new GitDetails(githubInfo.getRepoUrl(), branch, path);
newDetails.setPackedId(githubInfo.getPackedId());
return newDetails;
} else {
return null;
}
Expand Down
56 changes: 42 additions & 14 deletions src/main/java/org/commonwl/view/workflow/WorkflowService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,16 +19,6 @@

package org.commonwl.view.workflow;

import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Date;
import java.util.List;

import org.commonwl.view.cwl.CWLService;
import org.commonwl.view.cwl.CWLToolRunner;
import org.commonwl.view.cwl.CWLToolStatus;
Expand All @@ -40,6 +30,7 @@
import org.commonwl.view.researchobject.ROBundleNotFoundException;
import org.eclipse.jgit.api.Git;
import org.eclipse.jgit.api.errors.GitAPIException;
import org.eclipse.jgit.api.errors.RefNotFoundException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
Expand All @@ -48,6 +39,16 @@
import org.springframework.data.domain.Pageable;
import org.springframework.stereotype.Service;

import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Date;
import java.util.List;

@Service
public class WorkflowService {

Expand Down Expand Up @@ -193,9 +194,23 @@ public Workflow getWorkflow(GitDetails gitInfo) {
*/
public List<WorkflowOverview> getWorkflowsFromDirectory(GitDetails gitInfo) throws IOException, GitAPIException {
List<WorkflowOverview> workflowsInDir = new ArrayList<>();
boolean safeToAccess = gitSemaphore.acquire(gitInfo.getRepoUrl());
try {
Git repo = gitService.getRepository(gitInfo, safeToAccess);
boolean safeToAccess = gitSemaphore.acquire(gitInfo.getRepoUrl());
Git repo = null;
while (repo == null) {
try {
repo = gitService.getRepository(gitInfo, safeToAccess);
} catch (RefNotFoundException ex) {
// Attempt slashes in branch fix
GitDetails correctedForSlash = gitService.transferPathToBranch(gitInfo);
if (correctedForSlash != null) {
gitInfo = correctedForSlash;
} else {
throw ex;
}
}
}

Path localPath = repo.getRepository().getWorkTree().toPath();
Path pathToDirectory = localPath.resolve(gitInfo.getPath()).normalize().toAbsolutePath();
Path root = Paths.get("/").toAbsolutePath();
Expand Down Expand Up @@ -267,9 +282,22 @@ public QueuedWorkflow createQueuedWorkflow(GitDetails gitInfo)
throws GitAPIException, WorkflowNotFoundException, IOException {
QueuedWorkflow queuedWorkflow;

boolean safeToAccess = gitSemaphore.acquire(gitInfo.getRepoUrl());
try {
Git repo = gitService.getRepository(gitInfo, safeToAccess);
boolean safeToAccess = gitSemaphore.acquire(gitInfo.getRepoUrl());
Git repo = null;
while (repo == null) {
try {
repo = gitService.getRepository(gitInfo, safeToAccess);
} catch (RefNotFoundException ex) {
// Attempt slashes in branch fix
GitDetails correctedForSlash = gitService.transferPathToBranch(gitInfo);
if (correctedForSlash != null) {
gitInfo = correctedForSlash;
} else {
throw ex;
}
}
}
File localPath = repo.getRepository().getWorkTree();
String latestCommit = gitService.getCurrentCommitID(repo);

Expand Down